When the object detection algorithm is applied to the bird protection project, there are many problems like large model parameters, high similarity between bird species and single sample scene. In order to further improve the detection accuracy and stability of the object detection model, a multi-object detection algorithm for fine-grained birds is proposed. Firstly, the algorithm introduces Depthwise separable convolution into the feature extraction layer of YOLOv3 algorithm. The convolution process is divided into two parts: deep convolution and point-by-point convolution. The separation between intra-channel convolution and inter-channel convolution is realized. On the basis of high detection accuracy, the number of algorithm model parameters and calculation amount are greatly reduced. Finally, Focal loss was added to the loss function to solve the serious imbalance of positive and negative samples. By reducing the weight of the large number of simple background classes, the algorithm was more focused on detecting foreground classes. The experimental results show that, in the bird data set, the average precision mean (mAP) index of this algorithm is 2.71% higher than YOLOv3 algorithm, the number of parameters is 79.88% lower than YOLOv3 basic model, and the number of frames per second (FPS) is 19.98% higher than YOLOv3 algorithm. This algorithm not only greatly reduces the number of model parameters and computation, but also improves the detection speed and mAP.